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- PDB-9ypf: S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate -

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Basic information

Entry
Database: PDB / ID: 9ypf
TitleS. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate
Components
  • Cmp-binding-factor 1
  • RNA
KeywordsRNA BINDING PROTEIN/RNA / exonuclease / translation / RNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


rRNA 3'-end processing / exonuclease activity / nucleic acid binding
Similarity search - Function
: / HD domain profile. / HD domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Cmp-binding-factor 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMattingly, J.M. / Tanquary, J.R. / Dunham, C.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121359 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150986 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093278 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM8367 United States
CitationJournal: To Be Published
Title: Structural insights into RNA recognition by the Staphylococcus aureus exoribonuclease YhaM
Authors: Mattingly, J.M. / Tanquary, J.R. / Liponska, A. / Yap, M.N.F. / Dunham, C.M.
History
DepositionOct 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cmp-binding-factor 1
B: Cmp-binding-factor 1
C: Cmp-binding-factor 1
D: Cmp-binding-factor 1
E: Cmp-binding-factor 1
F: Cmp-binding-factor 1
G: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,21325
Polymers227,3517
Non-polymers86118
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cmp-binding-factor 1


Mass: 35785.797 Da / Num. of mol.: 6 / Mutation: D193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cbf1, SAUSA300_1791 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XHZ3
#2: RNA chain RNA


Mass: 12636.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrateCOMPLEX#20MULTIPLE SOURCES
2YhaM D193A hexamerCOMPLEX#11RECOMBINANT
3hairpin RNA substrateCOMPLEX#21SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Staphylococcus aureus (bacteria)1280
33Staphylococcus aureus (bacteria)1280
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium dihydrogen phosphateNaH2PO41
2150 mMsodium chlorideNaCl1
37 mMmagnesium chlorideMgCl21
41 % v/vglycerolC3H8O31
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 52.97 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15724
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.0particle selectioncryoSPARC Template Picker (following micrograph denoising with Micrograph Denoiser)
2Leginonimage acquisition
4cryoSPARC4.7.0CTF correctionPatch CTF Estimation
7UCSF ChimeraXmodel fitting
9cryoSPARC4.7.0initial Euler assignmentNon-Uniform Refinement
10cryoSPARC4.7.0final Euler assignmentNon-Uniform Refinement
11cryoSPARC4.7.0classificationcryoSPARC 3D Classication (without alignment)
12cryoSPARC4.7.03D reconstructionHomogeneous Reconstruct Only
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2080911
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42145 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingB value: 102 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: Initial model generated de novo using ModelAngelo / Source name: Other / Type: other

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